The entire farm yard is fenced with rail fencing and page wire farm fence. This keeps the birds in. Why I am not sure because within the farm yard, they will slip through the page wire into other critters pens. In spring I netted a whole section of page wire between the lambs and pigs. I know you understand why. Deer fence netting is annoying to the animals and they avoid it but I have found it has to be secure or they can also get caught in it. I use ties to secure it temporarily or wire or plastic twine for a more permanent project. The Muscovy ducks fly over their fenced pen, but only the girls. The male stays on his side. They are excellent fliers. Most of the chickens can fly over their 52 inch livestock panel and netting enclosure. Actually, maybe because of the bitter cold today, they finally stayed put. I did not let the turkeys out today...just couldn't do it. Yesterday they were on the cedar roof of my house.The turkeys are in a 16 x 8 foot turkey tractor and there are only 8 of them. I do feel sorry for them in summer and even though I move that tractor, they never get to do what turkeys love so I let them out. They fly into the goat pen, but cannot get out. They fly into the sheep pen, but cannot get out. Why, I just do not understand. One nearly met her demise when she flew into the Berkshire pen though and had I not been there to rescue her, she would have been their Thanksgiving dinner. The Bantams fly everywhere. They are the least problematic because they are people shy and avoid the house. Yay!
Each area has a house of some sort with a roof, so that cannot be the reason they want to be elsewhere.
Tara, your set up is very admirable. I have only been here since late March of 2011 and have much work to do to create spaces for the critters. I do use livestock panels a lot. Two of my dogs will jump any fence at all that I have except the 7 foot fence in one area. This is good and bad of course. No predators come near the critters, but I have lost 2 dogs to the highway who were fence jumpers. They learn that from each other (jumping).
It is frustrating to have the poo everywhere and I must say winter is very clean. The animals tend to stay in their yards except the Muscovy girls and the Bantams and I lock the turkeys in. I am going to try a solid slab fence at the house to fence in the yard. Maybe if they cannot see what is over on the other side, they will not be tempted to go there, but that will have to wait until next year. Sigh.